.mdstripped down
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.Rmdsingle document to integrate data analysis with textual representations, linking data, code, and text are not linked
– A documentantion language – A programming language
rmarkdown integrates R with md
Computational science has led to exciting new developments:
Increasing computational complexity of analyses:
the nature of the work has exposed limitations in our ability to evaluate published findings.
- Even basic analyses difficult to describe
Heavy computational requirements thrust upon people without adequate training in statistics and computing
Errors more easily introduced into long analysis pipelines
Knowledge transfer is inhibited
Results are difficult to replicate or reproduce
Complicated analyses cannot be trusted
Reproducibility has the potential to serve as a minimum standard for judging scientific claims when full independent replication of a study is not possible.
evdence needs:
rmarkdown is the glue that knits the tools, processes and output into evidence trails
at all stages of science
empower your code and data
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a <- 10 the value of parameter *a* is `r a`
the value of parameter a is 10


<img src="resources/cheat.png" width="200px" />
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[Johns Hopkins Bloomberg School of Public Health](http://www.jhsph.edu/)
[Download R](http://www.r-project.org/)
[RStudio](http://www.rstudio.com/)
.md resourcesR code chunks can be used as a means render R output into documents or to simply display code for illustration
for more details see http://yihui.name/knitr/
knitr::kable() tablesrequire(knitr)
data(airquality)
kable(airquality, caption = "New York Air Quality Measurements")| Ozone | Solar.R | Wind | Temp | Month | Day |
|---|---|---|---|---|---|
| 41 | 190 | 7.4 | 67 | 5 | 1 |
| 36 | 118 | 8.0 | 72 | 5 | 2 |
| 12 | 149 | 12.6 | 74 | 5 | 3 |
| 18 | 313 | 11.5 | 62 | 5 | 4 |
| NA | NA | 14.3 | 56 | 5 | 5 |
| 28 | NA | 14.9 | 66 | 5 | 6 |
| 23 | 299 | 8.6 | 65 | 5 | 7 |
| 19 | 99 | 13.8 | 59 | 5 | 8 |
| 8 | 19 | 20.1 | 61 | 5 | 9 |
| NA | 194 | 8.6 | 69 | 5 | 10 |
| 7 | NA | 6.9 | 74 | 5 | 11 |
| 16 | 256 | 9.7 | 69 | 5 | 12 |
| 11 | 290 | 9.2 | 66 | 5 | 13 |
| 14 | 274 | 10.9 | 68 | 5 | 14 |
| 18 | 65 | 13.2 | 58 | 5 | 15 |
| 14 | 334 | 11.5 | 64 | 5 | 16 |
| 34 | 307 | 12.0 | 66 | 5 | 17 |
| 6 | 78 | 18.4 | 57 | 5 | 18 |
| 30 | 322 | 11.5 | 68 | 5 | 19 |
| 11 | 44 | 9.7 | 62 | 5 | 20 |
| 1 | 8 | 9.7 | 59 | 5 | 21 |
| 11 | 320 | 16.6 | 73 | 5 | 22 |
| 4 | 25 | 9.7 | 61 | 5 | 23 |
| 32 | 92 | 12.0 | 61 | 5 | 24 |
| NA | 66 | 16.6 | 57 | 5 | 25 |
| NA | 266 | 14.9 | 58 | 5 | 26 |
| NA | NA | 8.0 | 57 | 5 | 27 |
| 23 | 13 | 12.0 | 67 | 5 | 28 |
| 45 | 252 | 14.9 | 81 | 5 | 29 |
| 115 | 223 | 5.7 | 79 | 5 | 30 |
| 37 | 279 | 7.4 | 76 | 5 | 31 |
| NA | 286 | 8.6 | 78 | 6 | 1 |
| NA | 287 | 9.7 | 74 | 6 | 2 |
| NA | 242 | 16.1 | 67 | 6 | 3 |
| NA | 186 | 9.2 | 84 | 6 | 4 |
| NA | 220 | 8.6 | 85 | 6 | 5 |
| NA | 264 | 14.3 | 79 | 6 | 6 |
| 29 | 127 | 9.7 | 82 | 6 | 7 |
| NA | 273 | 6.9 | 87 | 6 | 8 |
| 71 | 291 | 13.8 | 90 | 6 | 9 |
| 39 | 323 | 11.5 | 87 | 6 | 10 |
| NA | 259 | 10.9 | 93 | 6 | 11 |
| NA | 250 | 9.2 | 92 | 6 | 12 |
| 23 | 148 | 8.0 | 82 | 6 | 13 |
| NA | 332 | 13.8 | 80 | 6 | 14 |
| NA | 322 | 11.5 | 79 | 6 | 15 |
| 21 | 191 | 14.9 | 77 | 6 | 16 |
| 37 | 284 | 20.7 | 72 | 6 | 17 |
| 20 | 37 | 9.2 | 65 | 6 | 18 |
| 12 | 120 | 11.5 | 73 | 6 | 19 |
| 13 | 137 | 10.3 | 76 | 6 | 20 |
| NA | 150 | 6.3 | 77 | 6 | 21 |
| NA | 59 | 1.7 | 76 | 6 | 22 |
| NA | 91 | 4.6 | 76 | 6 | 23 |
| NA | 250 | 6.3 | 76 | 6 | 24 |
| NA | 135 | 8.0 | 75 | 6 | 25 |
| NA | 127 | 8.0 | 78 | 6 | 26 |
| NA | 47 | 10.3 | 73 | 6 | 27 |
| NA | 98 | 11.5 | 80 | 6 | 28 |
| NA | 31 | 14.9 | 77 | 6 | 29 |
| NA | 138 | 8.0 | 83 | 6 | 30 |
| 135 | 269 | 4.1 | 84 | 7 | 1 |
| 49 | 248 | 9.2 | 85 | 7 | 2 |
| 32 | 236 | 9.2 | 81 | 7 | 3 |
| NA | 101 | 10.9 | 84 | 7 | 4 |
| 64 | 175 | 4.6 | 83 | 7 | 5 |
| 40 | 314 | 10.9 | 83 | 7 | 6 |
| 77 | 276 | 5.1 | 88 | 7 | 7 |
| 97 | 267 | 6.3 | 92 | 7 | 8 |
| 97 | 272 | 5.7 | 92 | 7 | 9 |
| 85 | 175 | 7.4 | 89 | 7 | 10 |
| NA | 139 | 8.6 | 82 | 7 | 11 |
| 10 | 264 | 14.3 | 73 | 7 | 12 |
| 27 | 175 | 14.9 | 81 | 7 | 13 |
| NA | 291 | 14.9 | 91 | 7 | 14 |
| 7 | 48 | 14.3 | 80 | 7 | 15 |
| 48 | 260 | 6.9 | 81 | 7 | 16 |
| 35 | 274 | 10.3 | 82 | 7 | 17 |
| 61 | 285 | 6.3 | 84 | 7 | 18 |
| 79 | 187 | 5.1 | 87 | 7 | 19 |
| 63 | 220 | 11.5 | 85 | 7 | 20 |
| 16 | 7 | 6.9 | 74 | 7 | 21 |
| NA | 258 | 9.7 | 81 | 7 | 22 |
| NA | 295 | 11.5 | 82 | 7 | 23 |
| 80 | 294 | 8.6 | 86 | 7 | 24 |
| 108 | 223 | 8.0 | 85 | 7 | 25 |
| 20 | 81 | 8.6 | 82 | 7 | 26 |
| 52 | 82 | 12.0 | 86 | 7 | 27 |
| 82 | 213 | 7.4 | 88 | 7 | 28 |
| 50 | 275 | 7.4 | 86 | 7 | 29 |
| 64 | 253 | 7.4 | 83 | 7 | 30 |
| 59 | 254 | 9.2 | 81 | 7 | 31 |
| 39 | 83 | 6.9 | 81 | 8 | 1 |
| 9 | 24 | 13.8 | 81 | 8 | 2 |
| 16 | 77 | 7.4 | 82 | 8 | 3 |
| 78 | NA | 6.9 | 86 | 8 | 4 |
| 35 | NA | 7.4 | 85 | 8 | 5 |
| 66 | NA | 4.6 | 87 | 8 | 6 |
| 122 | 255 | 4.0 | 89 | 8 | 7 |
| 89 | 229 | 10.3 | 90 | 8 | 8 |
| 110 | 207 | 8.0 | 90 | 8 | 9 |
| NA | 222 | 8.6 | 92 | 8 | 10 |
| NA | 137 | 11.5 | 86 | 8 | 11 |
| 44 | 192 | 11.5 | 86 | 8 | 12 |
| 28 | 273 | 11.5 | 82 | 8 | 13 |
| 65 | 157 | 9.7 | 80 | 8 | 14 |
| NA | 64 | 11.5 | 79 | 8 | 15 |
| 22 | 71 | 10.3 | 77 | 8 | 16 |
| 59 | 51 | 6.3 | 79 | 8 | 17 |
| 23 | 115 | 7.4 | 76 | 8 | 18 |
| 31 | 244 | 10.9 | 78 | 8 | 19 |
| 44 | 190 | 10.3 | 78 | 8 | 20 |
| 21 | 259 | 15.5 | 77 | 8 | 21 |
| 9 | 36 | 14.3 | 72 | 8 | 22 |
| NA | 255 | 12.6 | 75 | 8 | 23 |
| 45 | 212 | 9.7 | 79 | 8 | 24 |
| 168 | 238 | 3.4 | 81 | 8 | 25 |
| 73 | 215 | 8.0 | 86 | 8 | 26 |
| NA | 153 | 5.7 | 88 | 8 | 27 |
| 76 | 203 | 9.7 | 97 | 8 | 28 |
| 118 | 225 | 2.3 | 94 | 8 | 29 |
| 84 | 237 | 6.3 | 96 | 8 | 30 |
| 85 | 188 | 6.3 | 94 | 8 | 31 |
| 96 | 167 | 6.9 | 91 | 9 | 1 |
| 78 | 197 | 5.1 | 92 | 9 | 2 |
| 73 | 183 | 2.8 | 93 | 9 | 3 |
| 91 | 189 | 4.6 | 93 | 9 | 4 |
| 47 | 95 | 7.4 | 87 | 9 | 5 |
| 32 | 92 | 15.5 | 84 | 9 | 6 |
| 20 | 252 | 10.9 | 80 | 9 | 7 |
| 23 | 220 | 10.3 | 78 | 9 | 8 |
| 21 | 230 | 10.9 | 75 | 9 | 9 |
| 24 | 259 | 9.7 | 73 | 9 | 10 |
| 44 | 236 | 14.9 | 81 | 9 | 11 |
| 21 | 259 | 15.5 | 76 | 9 | 12 |
| 28 | 238 | 6.3 | 77 | 9 | 13 |
| 9 | 24 | 10.9 | 71 | 9 | 14 |
| 13 | 112 | 11.5 | 71 | 9 | 15 |
| 46 | 237 | 6.9 | 78 | 9 | 16 |
| 18 | 224 | 13.8 | 67 | 9 | 17 |
| 13 | 27 | 10.3 | 76 | 9 | 18 |
| 24 | 238 | 10.3 | 68 | 9 | 19 |
| 16 | 201 | 8.0 | 82 | 9 | 20 |
| 13 | 238 | 12.6 | 64 | 9 | 21 |
| 23 | 14 | 9.2 | 71 | 9 | 22 |
| 36 | 139 | 10.3 | 81 | 9 | 23 |
| 7 | 49 | 10.3 | 69 | 9 | 24 |
| 14 | 20 | 16.6 | 63 | 9 | 25 |
| 30 | 193 | 6.9 | 70 | 9 | 26 |
| NA | 145 | 13.2 | 77 | 9 | 27 |
| 14 | 191 | 14.3 | 75 | 9 | 28 |
| 18 | 131 | 8.0 | 76 | 9 | 29 |
| 20 | 223 | 11.5 | 68 | 9 | 30 |
DT::kable() tablesrequire(DT)
data(airquality)
datatable(airquality, caption = "New York Air Quality Measurements")library(plotly)
set.seed(100)
d <- diamonds[sample(nrow(diamonds), 1000), ]
p <- ggplot(data = d, aes(x = carat, y = price)) +
geom_point(aes(text = paste("Clarity:", clarity)), size = 1) +
geom_smooth(aes(colour = cut, fill = cut)) + facet_wrap(~ cut)
ggplotly(p)create your first
.Rmd!
see my example: